Starting phenix.real_space_refine on Sun Jul 5 17:38:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q1e_72125/07_2026/9q1e_72125_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q1e_72125/07_2026/9q1e_72125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q1e_72125/07_2026/9q1e_72125_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q1e_72125/07_2026/9q1e_72125_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q1e_72125/07_2026/9q1e_72125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q1e_72125/07_2026/9q1e_72125.map" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 34 5.49 5 Mg 8 5.21 5 S 168 5.16 5 Be 4 3.05 5 C 18317 2.51 5 N 4424 2.21 5 O 5499 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28466 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6837 Classifications: {'peptide': 889} Link IDs: {'PTRANS': 32, 'TRANS': 856} Chain: "B" Number of atoms: 6837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6837 Classifications: {'peptide': 889} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 855} Chain: "C" Number of atoms: 6837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6837 Classifications: {'peptide': 889} Link IDs: {'PTRANS': 32, 'TRANS': 856} Chain: "D" Number of atoms: 6837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 889, 6837 Classifications: {'peptide': 889} Link IDs: {'PTRANS': 32, 'TRANS': 856} Chain: "A" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 249 Unusual residues: {' MG': 2, 'BEF': 1, 'CDL': 4, 'LMT': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 192 Chain: "B" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 353 Unusual residues: {' MG': 2, 'BEF': 1, 'CDL': 6, 'LMT': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 288 Chain: "C" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 336 Unusual residues: {' MG': 2, 'BEF': 1, 'CDL': 5, 'LMT': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 240 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {' MG': 2, 'BEF': 1, 'CDL': 2, 'LMT': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1 LMT A1001 " occ=0.00 ... (33 atoms not shown) pdb=" O6B LMT A1001 " occ=0.00 residue: pdb=" C1 LMT B1001 " occ=0.00 ... (33 atoms not shown) pdb=" O6B LMT B1001 " occ=0.00 residue: pdb=" C1 LMT C1002 " occ=0.00 ... (33 atoms not shown) pdb=" O6B LMT C1002 " occ=0.00 residue: pdb=" C1 LMT C1003 " occ=0.00 ... (33 atoms not shown) pdb=" O6B LMT C1003 " occ=0.00 residue: pdb=" C1 LMT D1001 " occ=0.00 ... (33 atoms not shown) pdb=" O6B LMT D1001 " occ=0.00 residue: pdb=" C1 LMT D1002 " occ=0.00 ... (33 atoms not shown) pdb=" O6B LMT D1002 " occ=0.00 Time building chain proxies: 6.77, per 1000 atoms: 0.24 Number of scatterers: 28466 At special positions: 0 Unit cell: (182.28, 222.27, 176.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 168 16.00 P 34 15.00 Mg 8 11.99 F 12 9.00 O 5499 8.00 N 4424 7.00 C 18317 6.00 Be 4 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.4 seconds 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6664 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 12 sheets defined 51.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 28 through 33 removed outlier: 4.374A pdb=" N SER A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 84 through 101 removed outlier: 4.000A pdb=" N ILE A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 134 removed outlier: 3.859A pdb=" N ILE A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 134 " --> pdb=" O PHE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.774A pdb=" N ALA A 191 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 300 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.609A pdb=" N ALA A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 345 through 354 removed outlier: 4.321A pdb=" N ILE A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'A' and resid 403 through 413 removed outlier: 3.728A pdb=" N ALA A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 409 " --> pdb=" O MET A 405 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 474 removed outlier: 3.502A pdb=" N ASP A 473 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 474 " --> pdb=" O MET A 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 470 through 474' Processing helix chain 'A' and resid 521 through 525 removed outlier: 4.224A pdb=" N PHE A 524 " --> pdb=" O ILE A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 Processing helix chain 'A' and resid 569 through 581 removed outlier: 3.608A pdb=" N THR A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 596 removed outlier: 4.030A pdb=" N ASP A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 596 " --> pdb=" O ASP A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 608 removed outlier: 4.000A pdb=" N ALA A 603 " --> pdb=" O ASN A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.801A pdb=" N ALA A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 649 Processing helix chain 'A' and resid 659 through 666 removed outlier: 3.531A pdb=" N LYS A 663 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 664 " --> pdb=" O ASP A 660 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 665 " --> pdb=" O ILE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 715 removed outlier: 3.882A pdb=" N LYS A 680 " --> pdb=" O MET A 676 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 738 Processing helix chain 'A' and resid 739 through 744 Proline residue: A 742 - end of helix No H-bonds generated for 'chain 'A' and resid 739 through 744' Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.592A pdb=" N LEU A 751 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 752 " --> pdb=" O GLU A 749 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 753 " --> pdb=" O TYR A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 787 removed outlier: 3.679A pdb=" N VAL A 762 " --> pdb=" O ASP A 758 " (cutoff:3.500A) Proline residue: A 771 - end of helix removed outlier: 3.528A pdb=" N SER A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N PHE A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 803 through 828 removed outlier: 3.591A pdb=" N VAL A 819 " --> pdb=" O THR A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 845 through 862 Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 879 through 907 removed outlier: 4.445A pdb=" N TRP A 883 " --> pdb=" O ASN A 879 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 896 " --> pdb=" O MET A 892 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE A 897 " --> pdb=" O MET A 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 30 Processing helix chain 'B' and resid 35 through 41 removed outlier: 3.702A pdb=" N LYS B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.993A pdb=" N SER B 45 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 61 removed outlier: 4.025A pdb=" N SER B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 84 through 102 Processing helix chain 'B' and resid 112 through 133 removed outlier: 3.686A pdb=" N GLU B 133 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 removed outlier: 4.264A pdb=" N ASN B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.639A pdb=" N LYS B 145 " --> pdb=" O ASN B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 3.514A pdb=" N ALA B 257 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 298 removed outlier: 3.637A pdb=" N SER B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 301 through 317 Processing helix chain 'B' and resid 320 through 338 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 348 through 354 Processing helix chain 'B' and resid 385 through 397 removed outlier: 3.551A pdb=" N LEU B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 396 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 418 removed outlier: 3.807A pdb=" N LEU B 407 " --> pdb=" O ASN B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.686A pdb=" N ARG B 492 " --> pdb=" O THR B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 506 removed outlier: 3.525A pdb=" N GLU B 504 " --> pdb=" O GLU B 501 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 505 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 523 Processing helix chain 'B' and resid 547 through 558 Processing helix chain 'B' and resid 569 through 580 removed outlier: 3.749A pdb=" N SER B 575 " --> pdb=" O LYS B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 606 Processing helix chain 'B' and resid 615 through 629 Processing helix chain 'B' and resid 641 through 648 removed outlier: 4.352A pdb=" N ALA B 645 " --> pdb=" O ASN B 641 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 665 removed outlier: 3.641A pdb=" N SER B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 714 removed outlier: 3.634A pdb=" N LYS B 680 " --> pdb=" O MET B 676 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 710 " --> pdb=" O ASN B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 738 Processing helix chain 'B' and resid 739 through 744 Proline residue: B 742 - end of helix No H-bonds generated for 'chain 'B' and resid 739 through 744' Processing helix chain 'B' and resid 747 through 751 Processing helix chain 'B' and resid 758 through 770 Processing helix chain 'B' and resid 770 through 787 removed outlier: 3.714A pdb=" N SER B 774 " --> pdb=" O GLY B 770 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE B 776 " --> pdb=" O THR B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 793 removed outlier: 4.033A pdb=" N THR B 792 " --> pdb=" O ILE B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 828 Processing helix chain 'B' and resid 828 through 833 Processing helix chain 'B' and resid 845 through 862 Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'B' and resid 879 through 907 removed outlier: 4.335A pdb=" N TRP B 883 " --> pdb=" O ASN B 879 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B 893 " --> pdb=" O VAL B 889 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 894 " --> pdb=" O MET B 890 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 32 removed outlier: 3.758A pdb=" N LEU C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 73 through 82 Processing helix chain 'C' and resid 84 through 102 Processing helix chain 'C' and resid 113 through 132 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.572A pdb=" N GLU C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 300 removed outlier: 3.781A pdb=" N GLU C 270 " --> pdb=" O LYS C 266 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 286 " --> pdb=" O ARG C 282 " (cutoff:3.500A) Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 301 through 317 removed outlier: 3.606A pdb=" N THR C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 338 removed outlier: 3.526A pdb=" N THR C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 338 " --> pdb=" O VAL C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 384 through 396 removed outlier: 3.933A pdb=" N LEU C 388 " --> pdb=" O ASN C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 416 Processing helix chain 'C' and resid 491 through 495 removed outlier: 3.676A pdb=" N ILE C 495 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 505 Processing helix chain 'C' and resid 527 through 532 removed outlier: 3.723A pdb=" N SER C 530 " --> pdb=" O GLN C 527 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU C 531 " --> pdb=" O ASP C 528 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET C 532 " --> pdb=" O GLU C 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 527 through 532' Processing helix chain 'C' and resid 552 through 558 Processing helix chain 'C' and resid 569 through 581 removed outlier: 3.787A pdb=" N THR C 573 " --> pdb=" O ASN C 569 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 574 " --> pdb=" O ASP C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 Processing helix chain 'C' and resid 600 through 608 removed outlier: 3.681A pdb=" N ALA C 607 " --> pdb=" O ALA C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 629 Processing helix chain 'C' and resid 641 through 648 removed outlier: 4.429A pdb=" N ALA C 645 " --> pdb=" O ASN C 641 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 648 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 693 removed outlier: 4.814A pdb=" N GLY C 685 " --> pdb=" O GLY C 681 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N THR C 688 " --> pdb=" O GLU C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 713 removed outlier: 3.530A pdb=" N VAL C 710 " --> pdb=" O ASN C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 738 Processing helix chain 'C' and resid 739 through 744 Proline residue: C 742 - end of helix No H-bonds generated for 'chain 'C' and resid 739 through 744' Processing helix chain 'C' and resid 747 through 751 Processing helix chain 'C' and resid 758 through 770 Processing helix chain 'C' and resid 770 through 775 removed outlier: 3.698A pdb=" N SER C 774 " --> pdb=" O GLY C 770 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 775 " --> pdb=" O PRO C 771 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 770 through 775' Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 803 through 828 Processing helix chain 'C' and resid 828 through 833 Processing helix chain 'C' and resid 845 through 862 Processing helix chain 'C' and resid 865 through 870 Processing helix chain 'C' and resid 877 through 879 No H-bonds generated for 'chain 'C' and resid 877 through 879' Processing helix chain 'C' and resid 880 through 907 removed outlier: 3.694A pdb=" N ILE C 897 " --> pdb=" O MET C 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 42 removed outlier: 3.903A pdb=" N PHE D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 61 removed outlier: 4.290A pdb=" N GLU D 55 " --> pdb=" O GLU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 102 Processing helix chain 'D' and resid 112 through 134 removed outlier: 3.558A pdb=" N ARG D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 removed outlier: 3.579A pdb=" N GLU D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA D 257 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS D 258 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 300 removed outlier: 3.516A pdb=" N SER D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 301 through 317 Processing helix chain 'D' and resid 320 through 326 Processing helix chain 'D' and resid 328 through 338 removed outlier: 3.772A pdb=" N LYS D 338 " --> pdb=" O VAL D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 354 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.993A pdb=" N THR D 365 " --> pdb=" O ASP D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 392 removed outlier: 3.724A pdb=" N PHE D 392 " --> pdb=" O LEU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 398 removed outlier: 4.007A pdb=" N GLN D 398 " --> pdb=" O ASN D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 417 Processing helix chain 'D' and resid 484 through 487 Processing helix chain 'D' and resid 488 through 500 removed outlier: 3.782A pdb=" N ARG D 492 " --> pdb=" O THR D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 Processing helix chain 'D' and resid 526 through 530 removed outlier: 4.106A pdb=" N SER D 530 " --> pdb=" O GLN D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 removed outlier: 3.536A pdb=" N TYR D 558 " --> pdb=" O ALA D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 597 removed outlier: 3.662A pdb=" N LEU D 596 " --> pdb=" O ASP D 592 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP D 597 " --> pdb=" O ILE D 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 592 through 597' Processing helix chain 'D' and resid 598 through 605 removed outlier: 3.516A pdb=" N ALA D 603 " --> pdb=" O ASN D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 623 removed outlier: 6.056A pdb=" N ARG D 621 " --> pdb=" O GLN D 617 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 623 " --> pdb=" O LYS D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 630 Processing helix chain 'D' and resid 642 through 649 removed outlier: 3.694A pdb=" N SER D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 666 Processing helix chain 'D' and resid 676 through 714 removed outlier: 3.970A pdb=" N LYS D 680 " --> pdb=" O MET D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 738 Processing helix chain 'D' and resid 739 through 744 Proline residue: D 742 - end of helix No H-bonds generated for 'chain 'D' and resid 739 through 744' Processing helix chain 'D' and resid 747 through 751 Processing helix chain 'D' and resid 758 through 787 removed outlier: 3.887A pdb=" N VAL D 762 " --> pdb=" O ASP D 758 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER D 763 " --> pdb=" O ALA D 759 " (cutoff:3.500A) Proline residue: D 771 - end of helix removed outlier: 3.508A pdb=" N SER D 774 " --> pdb=" O GLY D 770 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE D 776 " --> pdb=" O THR D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 793 removed outlier: 3.726A pdb=" N THR D 792 " --> pdb=" O ILE D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 828 removed outlier: 3.859A pdb=" N GLY D 808 " --> pdb=" O VAL D 804 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE D 810 " --> pdb=" O TYR D 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 828 through 833 Processing helix chain 'D' and resid 845 through 862 Processing helix chain 'D' and resid 865 through 871 Processing helix chain 'D' and resid 879 through 907 removed outlier: 4.403A pdb=" N TRP D 883 " --> pdb=" O ASN D 879 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET D 893 " --> pdb=" O VAL D 889 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 343 Processing sheet with id=AA2, first strand: chain 'A' and resid 610 through 611 removed outlier: 8.634A pdb=" N PHE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 564 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 358 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU A 565 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N THR A 360 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE A 357 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET A 636 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS A 359 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N ILE A 653 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR A 635 " --> pdb=" O ILE A 653 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 187 removed outlier: 3.683A pdb=" N VAL B 243 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 195 through 197 removed outlier: 4.068A pdb=" N ILE B 196 " --> pdb=" O VAL B 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 341 through 343 removed outlier: 6.219A pdb=" N GLY B 652 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU B 670 " --> pdb=" O GLY B 652 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER B 654 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N ILE B 653 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR B 635 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 357 " --> pdb=" O GLY B 634 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET B 636 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N CYS B 359 " --> pdb=" O MET B 636 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B 358 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU B 565 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N THR B 360 " --> pdb=" O LEU B 565 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 508 through 511 Processing sheet with id=AA7, first strand: chain 'C' and resid 150 through 153 Processing sheet with id=AA8, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AA9, first strand: chain 'C' and resid 341 through 343 removed outlier: 6.362A pdb=" N GLY C 652 " --> pdb=" O VAL C 668 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU C 670 " --> pdb=" O GLY C 652 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER C 654 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL C 633 " --> pdb=" O VAL C 651 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ILE C 653 " --> pdb=" O VAL C 633 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR C 635 " --> pdb=" O ILE C 653 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 448 through 449 Processing sheet with id=AB2, first strand: chain 'C' and resid 509 through 512 removed outlier: 3.630A pdb=" N VAL C 512 " --> pdb=" O GLY C 536 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY C 536 " --> pdb=" O VAL C 512 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 341 through 343 removed outlier: 6.357A pdb=" N GLY D 652 " --> pdb=" O VAL D 668 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU D 670 " --> pdb=" O GLY D 652 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER D 654 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU D 358 " --> pdb=" O LYS D 563 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU D 565 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR D 360 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N PHE D 611 " --> pdb=" O VAL D 562 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE D 564 " --> pdb=" O PHE D 611 " (cutoff:3.500A) 1155 hydrogen bonds defined for protein. 3390 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.65 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4601 1.32 - 1.44: 6882 1.44 - 1.57: 17044 1.57 - 1.69: 68 1.69 - 1.82: 324 Bond restraints: 28919 Sorted by residual: bond pdb=" F2 BEF C1001 " pdb="BE BEF C1001 " ideal model delta sigma weight residual 1.476 1.766 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" F2 BEF D1003 " pdb="BE BEF D1003 " ideal model delta sigma weight residual 1.476 1.766 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" F2 BEF A1002 " pdb="BE BEF A1002 " ideal model delta sigma weight residual 1.476 1.766 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" F2 BEF B1002 " pdb="BE BEF B1002 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" F3 BEF D1003 " pdb="BE BEF D1003 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 ... (remaining 28914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 17.13: 39066 17.13 - 34.26: 2 34.26 - 51.39: 0 51.39 - 68.51: 0 68.51 - 85.64: 1 Bond angle restraints: 39069 Sorted by residual: angle pdb=" C31 CDL B1006 " pdb=" CA7 CDL B1006 " pdb=" OA9 CDL B1006 " ideal model delta sigma weight residual 125.69 40.05 85.64 3.00e+00 1.11e-01 8.15e+02 angle pdb=" OA8 CDL B1006 " pdb=" CA7 CDL B1006 " pdb=" OA9 CDL B1006 " ideal model delta sigma weight residual 123.31 96.94 26.37 3.00e+00 1.11e-01 7.73e+01 angle pdb=" C31 CDL B1006 " pdb=" CA7 CDL B1006 " pdb=" OA8 CDL B1006 " ideal model delta sigma weight residual 110.96 136.99 -26.03 3.00e+00 1.11e-01 7.53e+01 angle pdb=" N VAL C 260 " pdb=" CA VAL C 260 " pdb=" C VAL C 260 " ideal model delta sigma weight residual 111.91 106.82 5.09 8.90e-01 1.26e+00 3.27e+01 angle pdb=" C SER A 158 " pdb=" CA SER A 158 " pdb=" CB SER A 158 " ideal model delta sigma weight residual 116.54 110.25 6.29 1.15e+00 7.56e-01 2.99e+01 ... (remaining 39064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 17031 35.65 - 71.30: 1199 71.30 - 106.94: 47 106.94 - 142.59: 5 142.59 - 178.24: 2 Dihedral angle restraints: 18284 sinusoidal: 7996 harmonic: 10288 Sorted by residual: dihedral pdb=" CA SER D 427 " pdb=" C SER D 427 " pdb=" N SER D 428 " pdb=" CA SER D 428 " ideal model delta harmonic sigma weight residual 180.00 152.79 27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ILE C 778 " pdb=" C ILE C 778 " pdb=" N THR C 779 " pdb=" CA THR C 779 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA MET C 692 " pdb=" C MET C 692 " pdb=" N ILE C 693 " pdb=" CA ILE C 693 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 18281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3637 0.051 - 0.102: 871 0.102 - 0.154: 129 0.154 - 0.205: 14 0.205 - 0.256: 7 Chirality restraints: 4658 Sorted by residual: chirality pdb=" CA LEU A 909 " pdb=" N LEU A 909 " pdb=" C LEU A 909 " pdb=" CB LEU A 909 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE B 23 " pdb=" CA ILE B 23 " pdb=" CG1 ILE B 23 " pdb=" CG2 ILE B 23 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLU A 908 " pdb=" N GLU A 908 " pdb=" C GLU A 908 " pdb=" CB GLU A 908 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 4655 not shown) Planarity restraints: 4772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 327 " 0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C THR A 327 " -0.067 2.00e-02 2.50e+03 pdb=" O THR A 327 " 0.025 2.00e-02 2.50e+03 pdb=" N CYS A 328 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 347 " -0.016 2.00e-02 2.50e+03 3.16e-02 1.00e+01 pdb=" C ASN B 347 " 0.055 2.00e-02 2.50e+03 pdb=" O ASN B 347 " -0.021 2.00e-02 2.50e+03 pdb=" N SER B 348 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 361 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C ASP B 361 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP B 361 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS B 362 " -0.014 2.00e-02 2.50e+03 ... (remaining 4769 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 8 1.93 - 2.67: 721 2.67 - 3.42: 41362 3.42 - 4.16: 64392 4.16 - 4.90: 116877 Nonbonded interactions: 223360 Sorted by model distance: nonbonded pdb=" CG2 THR A 363 " pdb=" F3 BEF A1002 " model vdw 1.190 3.410 nonbonded pdb=" OD1 ASP A 361 " pdb=" F1 BEF A1002 " model vdw 1.392 2.990 nonbonded pdb=" OG1 THR A 363 " pdb="MG MG A1004 " model vdw 1.445 2.170 nonbonded pdb=" OG1 THR D 363 " pdb=" F3 BEF D1003 " model vdw 1.501 2.990 nonbonded pdb=" O THR D 363 " pdb=" F2 BEF D1003 " model vdw 1.738 2.990 ... (remaining 223355 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 910 or resid 1004 or resid 1006 through 1007)) selection = (chain 'B' and (resid 22 through 910 or resid 1004 or resid 1006 through 1007)) selection = (chain 'C' and (resid 22 through 910 or resid 1004 or resid 1006 through 1007)) selection = (chain 'D' and (resid 22 through 910 or resid 1004 or resid 1006 through 1007)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.680 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.780 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.290 28919 Z= 0.386 Angle : 0.927 85.643 39069 Z= 0.425 Chirality : 0.044 0.256 4658 Planarity : 0.004 0.052 4772 Dihedral : 20.808 178.239 11620 Min Nonbonded Distance : 1.190 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.78 % Favored : 91.46 % Rotamer: Outliers : 2.45 % Allowed : 35.86 % Favored : 61.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3548 helix: 0.95 (0.14), residues: 1594 sheet: -0.78 (0.41), residues: 153 loop : -2.36 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 77 TYR 0.010 0.001 TYR D 806 PHE 0.028 0.001 PHE D 253 TRP 0.010 0.001 TRP D 817 HIS 0.014 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00767 / 0.39 (28919) covalent geometry : angle 0.92666 / 0.43 (39069) hydrogen bonds : bond 0.18816 / 12.61 ( 1155) hydrogen bonds : angle 6.51008 / 4.53 ( 3390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 196 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.5794 (tpt) cc_final: 0.5578 (tpt) REVERT: A 271 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7979 (mttm) REVERT: A 380 HIS cc_start: 0.4953 (OUTLIER) cc_final: 0.4033 (p90) REVERT: A 569 ASN cc_start: 0.8207 (p0) cc_final: 0.7897 (p0) REVERT: A 748 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8174 (tm-30) REVERT: B 146 MET cc_start: 0.6488 (pmt) cc_final: 0.5773 (tmm) REVERT: B 181 MET cc_start: 0.5806 (tpt) cc_final: 0.3093 (ptt) REVERT: B 258 LYS cc_start: 0.9373 (tptt) cc_final: 0.9047 (pttp) REVERT: B 447 VAL cc_start: -0.3731 (OUTLIER) cc_final: -0.3948 (t) REVERT: B 465 LYS cc_start: 0.2378 (OUTLIER) cc_final: 0.1543 (pptt) REVERT: B 507 MET cc_start: 0.6650 (mtp) cc_final: 0.5647 (pp-130) REVERT: B 532 MET cc_start: 0.2794 (ptp) cc_final: 0.2360 (ptp) REVERT: B 535 MET cc_start: -0.0899 (mtt) cc_final: -0.1310 (mpt) REVERT: C 347 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7936 (p0) REVERT: C 374 MET cc_start: 0.6757 (mpp) cc_final: 0.6263 (mtt) REVERT: C 471 MET cc_start: 0.3862 (tmt) cc_final: 0.2656 (mtp) REVERT: C 532 MET cc_start: 0.4948 (pp-130) cc_final: 0.3884 (ttp) REVERT: D 146 MET cc_start: -0.0255 (OUTLIER) cc_final: -0.0657 (mmt) REVERT: D 202 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7555 (p) REVERT: D 290 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8069 (t80) REVERT: D 374 MET cc_start: 0.0235 (mmp) cc_final: -0.0384 (mmt) REVERT: D 570 ASP cc_start: 0.8508 (t0) cc_final: 0.7750 (p0) REVERT: D 600 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.9014 (pm20) REVERT: D 647 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8087 (tppt) outliers start: 75 outliers final: 42 residues processed: 255 average time/residue: 0.6331 time to fit residues: 191.2942 Evaluate side-chains 242 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 390 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 709 SER Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 537 TYR Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 763 SER Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 442 ARG Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 625 THR Chi-restraints excluded: chain D residue 647 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 655 VAL Chi-restraints excluded: chain D residue 709 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 890 MET Chi-restraints excluded: chain D residue 895 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0370 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 7.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 398 GLN B 142 ASN B 390 HIS B 503 ASN B 569 ASN ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 390 HIS D 595 GLN D 618 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.174842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.107067 restraints weight = 50910.020| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.10 r_work: 0.3226 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28919 Z= 0.136 Angle : 0.755 47.263 39069 Z= 0.350 Chirality : 0.043 0.262 4658 Planarity : 0.004 0.047 4772 Dihedral : 16.893 171.137 5228 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.20 % Favored : 91.12 % Rotamer: Outliers : 4.16 % Allowed : 31.71 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.14), residues: 3548 helix: 1.25 (0.13), residues: 1640 sheet: -0.71 (0.41), residues: 157 loop : -2.38 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 77 TYR 0.013 0.001 TYR B 806 PHE 0.026 0.001 PHE A 818 TRP 0.009 0.001 TRP C 278 HIS 0.013 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (28919) covalent geometry : angle 0.75480 / 0.35 (39069) hydrogen bonds : bond 0.04835 / 3.24 ( 1155) hydrogen bonds : angle 4.80028 / 3.39 ( 3390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 202 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.5934 (tpt) cc_final: 0.5668 (tpt) REVERT: A 380 HIS cc_start: 0.4987 (OUTLIER) cc_final: 0.4069 (p90) REVERT: A 529 GLU cc_start: 0.5346 (OUTLIER) cc_final: 0.4630 (mm-30) REVERT: A 569 ASN cc_start: 0.8270 (p0) cc_final: 0.7945 (p0) REVERT: A 730 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8100 (tp) REVERT: A 748 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8184 (tm-30) REVERT: B 142 ASN cc_start: 0.4972 (OUTLIER) cc_final: 0.4705 (p0) REVERT: B 146 MET cc_start: 0.6551 (pmt) cc_final: 0.5827 (tmm) REVERT: B 258 LYS cc_start: 0.9424 (tptt) cc_final: 0.9100 (mtpt) REVERT: B 342 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 374 MET cc_start: 0.0669 (mmm) cc_final: 0.0439 (mmm) REVERT: B 447 VAL cc_start: -0.3303 (OUTLIER) cc_final: -0.3520 (t) REVERT: B 507 MET cc_start: 0.6771 (mtp) cc_final: 0.5754 (pp-130) REVERT: B 532 MET cc_start: 0.2829 (ptp) cc_final: 0.2478 (ptp) REVERT: B 535 MET cc_start: -0.0906 (OUTLIER) cc_final: -0.1324 (mpt) REVERT: C 270 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: C 471 MET cc_start: 0.4026 (tmt) cc_final: 0.2791 (mtp) REVERT: C 532 MET cc_start: 0.5050 (pp-130) cc_final: 0.4063 (ttp) REVERT: D 146 MET cc_start: 0.0017 (OUTLIER) cc_final: -0.0313 (mmt) REVERT: D 290 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8104 (t80) REVERT: D 374 MET cc_start: 0.0384 (mmp) cc_final: -0.0223 (mmt) REVERT: D 570 ASP cc_start: 0.8506 (t0) cc_final: 0.7635 (p0) REVERT: D 600 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8910 (pm20) REVERT: D 647 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8040 (tppt) outliers start: 127 outliers final: 35 residues processed: 307 average time/residue: 0.6105 time to fit residues: 222.4244 Evaluate side-chains 235 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 683 ILE Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 647 LYS Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 810 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 333 optimal weight: 0.8980 chunk 257 optimal weight: 0.9990 chunk 306 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 90 optimal weight: 0.4980 chunk 296 optimal weight: 2.9990 chunk 26 optimal weight: 0.0570 chunk 235 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN B 825 GLN C 60 GLN C 154 HIS C 347 ASN ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 618 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.173077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106015 restraints weight = 51464.362| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.02 r_work: 0.3184 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28919 Z= 0.126 Angle : 0.733 46.775 39069 Z= 0.336 Chirality : 0.043 0.263 4658 Planarity : 0.004 0.047 4772 Dihedral : 15.487 170.362 5174 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.72 % Favored : 91.66 % Rotamer: Outliers : 4.91 % Allowed : 29.97 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.14), residues: 3548 helix: 1.32 (0.14), residues: 1641 sheet: -0.37 (0.43), residues: 149 loop : -2.31 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 58 TYR 0.013 0.001 TYR C 806 PHE 0.022 0.001 PHE A 818 TRP 0.008 0.001 TRP C 302 HIS 0.010 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (28919) covalent geometry : angle 0.73288 / 0.34 (39069) hydrogen bonds : bond 0.04279 / 2.87 ( 1155) hydrogen bonds : angle 4.61035 / 3.26 ( 3390) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 193 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.1897 (OUTLIER) cc_final: 0.1652 (mt) REVERT: A 181 MET cc_start: 0.6026 (tpt) cc_final: 0.5765 (tpt) REVERT: A 380 HIS cc_start: 0.5061 (OUTLIER) cc_final: 0.4256 (p90) REVERT: A 419 LYS cc_start: 0.0801 (OUTLIER) cc_final: 0.0009 (pptt) REVERT: A 479 GLU cc_start: 0.1808 (OUTLIER) cc_final: -0.2050 (tt0) REVERT: A 529 GLU cc_start: 0.5154 (OUTLIER) cc_final: 0.4450 (mm-30) REVERT: A 569 ASN cc_start: 0.8275 (p0) cc_final: 0.7942 (p0) REVERT: A 571 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8032 (tttm) REVERT: A 730 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8058 (tp) REVERT: A 748 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8159 (tm-30) REVERT: B 146 MET cc_start: 0.6463 (pmt) cc_final: 0.5730 (tmm) REVERT: B 181 MET cc_start: 0.5884 (tpt) cc_final: 0.3065 (ptt) REVERT: B 231 MET cc_start: 0.3920 (tmm) cc_final: 0.3492 (tmm) REVERT: B 258 LYS cc_start: 0.9408 (tptt) cc_final: 0.9059 (mtpt) REVERT: B 374 MET cc_start: 0.0473 (mmm) cc_final: 0.0246 (mmm) REVERT: B 447 VAL cc_start: -0.3269 (OUTLIER) cc_final: -0.3492 (t) REVERT: B 507 MET cc_start: 0.6829 (mtp) cc_final: 0.5890 (pp-130) REVERT: B 532 MET cc_start: 0.3093 (ptp) cc_final: 0.2866 (ptp) REVERT: B 535 MET cc_start: -0.0788 (OUTLIER) cc_final: -0.1328 (mpt) REVERT: C 270 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: C 471 MET cc_start: 0.4195 (tmt) cc_final: 0.3122 (mtt) REVERT: C 532 MET cc_start: 0.5196 (pp-130) cc_final: 0.4271 (ttp) REVERT: D 146 MET cc_start: -0.0153 (OUTLIER) cc_final: -0.0441 (mmt) REVERT: D 231 MET cc_start: 0.4964 (OUTLIER) cc_final: 0.2359 (mmt) REVERT: D 290 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8078 (t80) REVERT: D 374 MET cc_start: 0.0496 (mmp) cc_final: 0.0272 (mmt) REVERT: D 423 LEU cc_start: 0.4943 (OUTLIER) cc_final: 0.4646 (mm) REVERT: D 445 MET cc_start: 0.7852 (mtp) cc_final: 0.7196 (ppp) REVERT: D 462 MET cc_start: 0.2629 (ptm) cc_final: 0.2221 (ppp) REVERT: D 498 LYS cc_start: -0.1928 (OUTLIER) cc_final: -0.2157 (pptt) REVERT: D 535 MET cc_start: 0.1015 (ptt) cc_final: -0.0150 (mtt) REVERT: D 570 ASP cc_start: 0.8510 (t0) cc_final: 0.7621 (p0) REVERT: D 600 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.9025 (pm20) outliers start: 150 outliers final: 46 residues processed: 314 average time/residue: 0.5606 time to fit residues: 210.3833 Evaluate side-chains 250 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 831 MET Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 498 LYS Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 646 MET Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain D residue 800 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 13 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 213 optimal weight: 0.0970 chunk 18 optimal weight: 20.0000 chunk 351 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 246 optimal weight: 0.9980 chunk 347 optimal weight: 0.9980 chunk 280 optimal weight: 20.0000 chunk 220 optimal weight: 0.0070 chunk 261 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 618 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.172085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.105249 restraints weight = 51655.421| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.95 r_work: 0.3192 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28919 Z= 0.118 Angle : 0.721 46.550 39069 Z= 0.329 Chirality : 0.042 0.263 4658 Planarity : 0.004 0.047 4772 Dihedral : 14.557 170.621 5166 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.06 % Favored : 91.32 % Rotamer: Outliers : 4.42 % Allowed : 30.30 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.14), residues: 3548 helix: 1.47 (0.14), residues: 1619 sheet: -0.33 (0.44), residues: 149 loop : -2.24 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 58 TYR 0.012 0.001 TYR C 806 PHE 0.021 0.001 PHE A 818 TRP 0.009 0.001 TRP C 302 HIS 0.012 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (28919) covalent geometry : angle 0.72116 / 0.33 (39069) hydrogen bonds : bond 0.03936 / 2.64 ( 1155) hydrogen bonds : angle 4.45741 / 3.15 ( 3390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 196 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.2130 (OUTLIER) cc_final: 0.1896 (mt) REVERT: A 181 MET cc_start: 0.5855 (tpt) cc_final: 0.5600 (tpt) REVERT: A 380 HIS cc_start: 0.5002 (OUTLIER) cc_final: 0.4259 (p90) REVERT: A 479 GLU cc_start: 0.1919 (OUTLIER) cc_final: -0.1967 (tt0) REVERT: A 529 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.4643 (mm-30) REVERT: A 569 ASN cc_start: 0.8307 (p0) cc_final: 0.7984 (p0) REVERT: A 571 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8037 (tttm) REVERT: A 730 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8074 (tp) REVERT: A 748 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8109 (tm-30) REVERT: B 146 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5891 (pp-130) REVERT: B 181 MET cc_start: 0.5805 (tpt) cc_final: 0.2856 (ptt) REVERT: B 231 MET cc_start: 0.3682 (tmm) cc_final: 0.3325 (tmm) REVERT: B 258 LYS cc_start: 0.9413 (tptt) cc_final: 0.9069 (mtpt) REVERT: B 374 MET cc_start: 0.0333 (mmm) cc_final: 0.0045 (mmm) REVERT: B 447 VAL cc_start: -0.3598 (OUTLIER) cc_final: -0.3820 (t) REVERT: B 507 MET cc_start: 0.6864 (mtp) cc_final: 0.5870 (pp-130) REVERT: B 535 MET cc_start: -0.0861 (OUTLIER) cc_final: -0.1408 (mpt) REVERT: C 471 MET cc_start: 0.4154 (tmt) cc_final: 0.3151 (mtt) REVERT: C 532 MET cc_start: 0.5351 (pp-130) cc_final: 0.4574 (ttp) REVERT: D 37 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: D 146 MET cc_start: -0.0172 (OUTLIER) cc_final: -0.0467 (mmt) REVERT: D 231 MET cc_start: 0.4896 (OUTLIER) cc_final: 0.2344 (mmt) REVERT: D 290 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8125 (t80) REVERT: D 423 LEU cc_start: 0.4950 (OUTLIER) cc_final: 0.4641 (mm) REVERT: D 445 MET cc_start: 0.7858 (mtp) cc_final: 0.7187 (ppp) REVERT: D 535 MET cc_start: 0.1063 (ptt) cc_final: -0.0142 (mtt) REVERT: D 570 ASP cc_start: 0.8501 (t0) cc_final: 0.7601 (p0) REVERT: D 600 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.9037 (pm20) REVERT: D 676 MET cc_start: 0.8630 (tpt) cc_final: 0.8421 (mmp) outliers start: 135 outliers final: 55 residues processed: 308 average time/residue: 0.5846 time to fit residues: 214.5869 Evaluate side-chains 260 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 190 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 749 GLU Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 600 GLU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 656 ASP Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain D residue 800 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 0 optimal weight: 30.0000 chunk 142 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 310 optimal weight: 0.0670 chunk 90 optimal weight: 20.0000 chunk 137 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 286 optimal weight: 3.9990 chunk 285 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN ** C 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.171659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.104452 restraints weight = 51422.724| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.97 r_work: 0.3168 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28919 Z= 0.136 Angle : 0.737 46.524 39069 Z= 0.335 Chirality : 0.043 0.262 4658 Planarity : 0.004 0.050 4772 Dihedral : 13.964 170.665 5165 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.92 % Favored : 91.54 % Rotamer: Outliers : 4.45 % Allowed : 30.33 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3548 helix: 1.50 (0.14), residues: 1617 sheet: -0.26 (0.44), residues: 150 loop : -2.24 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 686 TYR 0.014 0.001 TYR C 781 PHE 0.027 0.001 PHE D 253 TRP 0.009 0.001 TRP C 302 HIS 0.011 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (28919) covalent geometry : angle 0.73698 / 0.34 (39069) hydrogen bonds : bond 0.04170 / 2.80 ( 1155) hydrogen bonds : angle 4.45712 / 3.14 ( 3390) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 190 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.1970 (OUTLIER) cc_final: 0.1753 (mt) REVERT: A 181 MET cc_start: 0.5962 (tpt) cc_final: 0.5646 (tpt) REVERT: A 380 HIS cc_start: 0.4967 (OUTLIER) cc_final: 0.4190 (p90) REVERT: A 479 GLU cc_start: 0.1828 (OUTLIER) cc_final: -0.2060 (tt0) REVERT: A 529 GLU cc_start: 0.5371 (OUTLIER) cc_final: 0.4561 (mm-30) REVERT: A 569 ASN cc_start: 0.8257 (p0) cc_final: 0.7934 (p0) REVERT: A 571 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7994 (tttm) REVERT: A 730 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8064 (tp) REVERT: A 748 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8156 (tm-30) REVERT: B 31 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5219 (mmmt) REVERT: B 146 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.5951 (pp-130) REVERT: B 181 MET cc_start: 0.5899 (tpt) cc_final: 0.3001 (ptt) REVERT: B 231 MET cc_start: 0.3623 (tmm) cc_final: 0.3320 (tmm) REVERT: B 258 LYS cc_start: 0.9388 (tptt) cc_final: 0.9037 (mtpt) REVERT: B 447 VAL cc_start: -0.3596 (OUTLIER) cc_final: -0.3820 (t) REVERT: B 535 MET cc_start: -0.0887 (OUTLIER) cc_final: -0.1477 (mpt) REVERT: C 374 MET cc_start: 0.5030 (OUTLIER) cc_final: 0.4795 (mtt) REVERT: C 471 MET cc_start: 0.3872 (tmt) cc_final: 0.2851 (mtt) REVERT: C 505 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8296 (pp20) REVERT: C 532 MET cc_start: 0.5402 (pp-130) cc_final: 0.4732 (ttp) REVERT: D 37 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: D 146 MET cc_start: -0.0153 (OUTLIER) cc_final: -0.0435 (mmm) REVERT: D 231 MET cc_start: 0.4779 (OUTLIER) cc_final: 0.2302 (mmt) REVERT: D 290 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8125 (t80) REVERT: D 423 LEU cc_start: 0.5172 (OUTLIER) cc_final: 0.4858 (mm) REVERT: D 445 MET cc_start: 0.7888 (mtp) cc_final: 0.7211 (ppp) REVERT: D 535 MET cc_start: 0.1187 (ptt) cc_final: -0.0069 (mtt) REVERT: D 538 LEU cc_start: 0.3528 (OUTLIER) cc_final: 0.2664 (tm) REVERT: D 570 ASP cc_start: 0.8543 (t0) cc_final: 0.7691 (p0) REVERT: D 831 MET cc_start: 0.9149 (tpp) cc_final: 0.8911 (mmm) outliers start: 136 outliers final: 56 residues processed: 303 average time/residue: 0.6179 time to fit residues: 222.7904 Evaluate side-chains 261 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 187 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 656 ASP Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain D residue 800 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 39 optimal weight: 10.0000 chunk 96 optimal weight: 0.2980 chunk 300 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 ASN C 390 HIS ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.181719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.115181 restraints weight = 50444.286| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.92 r_work: 0.3256 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28919 Z= 0.122 Angle : 0.724 46.499 39069 Z= 0.330 Chirality : 0.042 0.262 4658 Planarity : 0.004 0.048 4772 Dihedral : 13.413 172.543 5160 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.98 % Favored : 91.46 % Rotamer: Outliers : 4.25 % Allowed : 30.24 % Favored : 65.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.15), residues: 3548 helix: 1.57 (0.14), residues: 1607 sheet: -0.20 (0.44), residues: 149 loop : -2.17 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 686 TYR 0.012 0.001 TYR C 781 PHE 0.020 0.001 PHE A 818 TRP 0.009 0.001 TRP C 302 HIS 0.011 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (28919) covalent geometry : angle 0.72431 / 0.33 (39069) hydrogen bonds : bond 0.03937 / 2.65 ( 1155) hydrogen bonds : angle 4.37981 / 3.09 ( 3390) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 192 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.1970 (OUTLIER) cc_final: 0.1757 (mt) REVERT: A 181 MET cc_start: 0.5934 (tpt) cc_final: 0.5710 (tpt) REVERT: A 380 HIS cc_start: 0.5018 (OUTLIER) cc_final: 0.4311 (p90) REVERT: A 479 GLU cc_start: 0.1750 (OUTLIER) cc_final: -0.2114 (tt0) REVERT: A 529 GLU cc_start: 0.5461 (OUTLIER) cc_final: 0.4759 (mm-30) REVERT: A 553 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8261 (ptpp) REVERT: A 569 ASN cc_start: 0.8249 (p0) cc_final: 0.7916 (p0) REVERT: A 571 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7994 (tttm) REVERT: A 730 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8121 (tp) REVERT: A 748 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8132 (tm-30) REVERT: B 31 LYS cc_start: 0.5740 (OUTLIER) cc_final: 0.5200 (mmmt) REVERT: B 146 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.5919 (pp-130) REVERT: B 258 LYS cc_start: 0.9392 (tptt) cc_final: 0.9048 (mtpt) REVERT: B 447 VAL cc_start: -0.3310 (OUTLIER) cc_final: -0.3518 (t) REVERT: B 535 MET cc_start: -0.0836 (OUTLIER) cc_final: -0.1355 (mpt) REVERT: B 748 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8024 (tp30) REVERT: C 270 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: C 374 MET cc_start: 0.5115 (mtt) cc_final: 0.4824 (mtt) REVERT: C 471 MET cc_start: 0.3797 (tmt) cc_final: 0.2803 (mtt) REVERT: C 532 MET cc_start: 0.5572 (pp-130) cc_final: 0.4953 (ttp) REVERT: D 37 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6660 (tm-30) REVERT: D 146 MET cc_start: -0.0137 (OUTLIER) cc_final: -0.0468 (mmm) REVERT: D 231 MET cc_start: 0.4448 (mtm) cc_final: 0.2163 (mmt) REVERT: D 290 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8128 (t80) REVERT: D 423 LEU cc_start: 0.5216 (OUTLIER) cc_final: 0.4858 (mm) REVERT: D 445 MET cc_start: 0.7848 (mtp) cc_final: 0.7175 (ppp) REVERT: D 535 MET cc_start: 0.1516 (ptt) cc_final: 0.0206 (mtt) REVERT: D 538 LEU cc_start: 0.3617 (OUTLIER) cc_final: 0.2681 (tm) REVERT: D 570 ASP cc_start: 0.8510 (t0) cc_final: 0.7648 (p0) REVERT: D 676 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8629 (mmp) outliers start: 130 outliers final: 54 residues processed: 297 average time/residue: 0.6186 time to fit residues: 218.3214 Evaluate side-chains 261 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 189 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 575 SER Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 749 GLU Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 656 ASP Chi-restraints excluded: chain D residue 676 MET Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 895 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 212 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.0070 chunk 260 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 331 optimal weight: 0.5980 chunk 202 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 HIS ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.183841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.117193 restraints weight = 50702.245| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.16 r_work: 0.3269 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28919 Z= 0.114 Angle : 0.728 46.461 39069 Z= 0.330 Chirality : 0.042 0.262 4658 Planarity : 0.004 0.047 4772 Dihedral : 13.004 172.846 5160 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.95 % Favored : 91.49 % Rotamer: Outliers : 3.40 % Allowed : 31.35 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 3548 helix: 1.62 (0.14), residues: 1611 sheet: -0.09 (0.45), residues: 149 loop : -2.14 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 444 TYR 0.012 0.001 TYR C 806 PHE 0.026 0.001 PHE D 253 TRP 0.010 0.001 TRP D 817 HIS 0.011 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (28919) covalent geometry : angle 0.72844 / 0.33 (39069) hydrogen bonds : bond 0.03739 / 2.53 ( 1155) hydrogen bonds : angle 4.34152 / 3.05 ( 3390) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 196 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.1887 (OUTLIER) cc_final: 0.1682 (mt) REVERT: A 181 MET cc_start: 0.5839 (tpt) cc_final: 0.5506 (tpt) REVERT: A 380 HIS cc_start: 0.4881 (OUTLIER) cc_final: 0.4294 (p90) REVERT: A 479 GLU cc_start: 0.1763 (OUTLIER) cc_final: -0.2107 (tt0) REVERT: A 529 GLU cc_start: 0.5485 (OUTLIER) cc_final: 0.4864 (mm-30) REVERT: A 553 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8260 (ptpp) REVERT: A 569 ASN cc_start: 0.8267 (p0) cc_final: 0.7926 (p0) REVERT: A 571 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7935 (ttmm) REVERT: A 730 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8116 (tp) REVERT: A 748 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8100 (tm-30) REVERT: B 31 LYS cc_start: 0.5773 (OUTLIER) cc_final: 0.5214 (mmmt) REVERT: B 146 MET cc_start: 0.6586 (pmt) cc_final: 0.5931 (pp-130) REVERT: B 181 MET cc_start: 0.5844 (tpt) cc_final: 0.3124 (ptt) REVERT: B 253 PHE cc_start: 0.4521 (t80) cc_final: 0.4219 (t80) REVERT: B 258 LYS cc_start: 0.9390 (tptt) cc_final: 0.9033 (mtpt) REVERT: B 376 HIS cc_start: 0.1874 (OUTLIER) cc_final: 0.1475 (p90) REVERT: B 447 VAL cc_start: -0.3351 (OUTLIER) cc_final: -0.3558 (t) REVERT: B 507 MET cc_start: 0.7066 (tpt) cc_final: 0.4783 (tmm) REVERT: B 535 MET cc_start: -0.0840 (OUTLIER) cc_final: -0.1328 (mpt) REVERT: B 748 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8021 (tp30) REVERT: C 270 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: C 350 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: C 376 HIS cc_start: 0.4756 (OUTLIER) cc_final: 0.4473 (p90) REVERT: C 471 MET cc_start: 0.3659 (tmt) cc_final: 0.2708 (mtt) REVERT: C 503 ASN cc_start: 0.8644 (t0) cc_final: 0.8230 (m-40) REVERT: C 505 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8408 (pp20) REVERT: C 532 MET cc_start: 0.5870 (pp-130) cc_final: 0.5422 (ttp) REVERT: D 37 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6642 (tm-30) REVERT: D 146 MET cc_start: -0.0134 (OUTLIER) cc_final: -0.0443 (mmm) REVERT: D 231 MET cc_start: 0.4481 (OUTLIER) cc_final: 0.2337 (mmt) REVERT: D 423 LEU cc_start: 0.5177 (OUTLIER) cc_final: 0.4852 (mm) REVERT: D 445 MET cc_start: 0.7848 (mtp) cc_final: 0.7193 (ppp) REVERT: D 535 MET cc_start: 0.1351 (ptt) cc_final: -0.0008 (mtt) REVERT: D 538 LEU cc_start: 0.3614 (OUTLIER) cc_final: 0.2678 (tm) REVERT: D 570 ASP cc_start: 0.8516 (t0) cc_final: 0.7753 (p0) outliers start: 104 outliers final: 57 residues processed: 284 average time/residue: 0.6277 time to fit residues: 212.5590 Evaluate side-chains 267 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 190 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 749 GLU Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 656 ASP Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 895 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 288 optimal weight: 0.3980 chunk 195 optimal weight: 4.9990 chunk 165 optimal weight: 0.3980 chunk 255 optimal weight: 0.5980 chunk 267 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 194 optimal weight: 9.9990 chunk 325 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 HIS ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.182251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.115548 restraints weight = 50949.748| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.01 r_work: 0.3267 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28919 Z= 0.118 Angle : 0.731 46.455 39069 Z= 0.332 Chirality : 0.042 0.262 4658 Planarity : 0.004 0.049 4772 Dihedral : 12.768 172.472 5157 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.92 % Favored : 91.49 % Rotamer: Outliers : 3.60 % Allowed : 31.09 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3548 helix: 1.63 (0.14), residues: 1615 sheet: -0.01 (0.45), residues: 149 loop : -2.14 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 443 TYR 0.012 0.001 TYR C 806 PHE 0.018 0.001 PHE A 818 TRP 0.009 0.001 TRP D 817 HIS 0.019 0.001 HIS C 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (28919) covalent geometry : angle 0.73141 / 0.33 (39069) hydrogen bonds : bond 0.03765 / 2.54 ( 1155) hydrogen bonds : angle 4.33144 / 3.05 ( 3390) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 190 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.1965 (OUTLIER) cc_final: 0.1750 (mt) REVERT: A 181 MET cc_start: 0.5988 (tpt) cc_final: 0.5635 (tpt) REVERT: A 380 HIS cc_start: 0.4909 (OUTLIER) cc_final: 0.4345 (p90) REVERT: A 479 GLU cc_start: 0.1778 (OUTLIER) cc_final: -0.2067 (tt0) REVERT: A 529 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.4862 (mm-30) REVERT: A 553 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8268 (ptpp) REVERT: A 569 ASN cc_start: 0.8279 (p0) cc_final: 0.7942 (p0) REVERT: A 571 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7938 (ttmm) REVERT: A 730 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8094 (tp) REVERT: A 748 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8108 (tm-30) REVERT: B 31 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.5259 (mmmt) REVERT: B 146 MET cc_start: 0.6582 (pmt) cc_final: 0.5889 (pp-130) REVERT: B 181 MET cc_start: 0.5807 (tpt) cc_final: 0.3031 (ptt) REVERT: B 258 LYS cc_start: 0.9398 (tptt) cc_final: 0.9042 (mtpt) REVERT: B 376 HIS cc_start: 0.1997 (OUTLIER) cc_final: 0.1645 (p90) REVERT: B 507 MET cc_start: 0.7269 (tpt) cc_final: 0.4930 (tmm) REVERT: B 535 MET cc_start: -0.0853 (OUTLIER) cc_final: -0.1337 (mpt) REVERT: B 748 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8012 (tp30) REVERT: C 270 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: C 350 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: C 376 HIS cc_start: 0.4672 (OUTLIER) cc_final: 0.4428 (p90) REVERT: C 471 MET cc_start: 0.3632 (tmt) cc_final: 0.2563 (ptp) REVERT: C 503 ASN cc_start: 0.8656 (t0) cc_final: 0.8263 (m-40) REVERT: C 505 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8416 (pp20) REVERT: C 532 MET cc_start: 0.5825 (pp-130) cc_final: 0.5440 (ttp) REVERT: D 37 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6649 (tm-30) REVERT: D 231 MET cc_start: 0.4408 (OUTLIER) cc_final: 0.2309 (mmt) REVERT: D 290 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8095 (t80) REVERT: D 423 LEU cc_start: 0.5125 (OUTLIER) cc_final: 0.4816 (mm) REVERT: D 445 MET cc_start: 0.7857 (mtp) cc_final: 0.7184 (ppp) REVERT: D 535 MET cc_start: 0.1344 (ptt) cc_final: -0.0073 (mtt) REVERT: D 538 LEU cc_start: 0.3611 (OUTLIER) cc_final: 0.2677 (tm) REVERT: D 570 ASP cc_start: 0.8515 (t0) cc_final: 0.7666 (p0) outliers start: 110 outliers final: 59 residues processed: 282 average time/residue: 0.5792 time to fit residues: 194.5786 Evaluate side-chains 268 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 190 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 376 HIS Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 749 GLU Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 656 ASP Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 895 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 273 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 335 optimal weight: 1.9990 chunk 14 optimal weight: 0.0030 chunk 158 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 303 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 278 optimal weight: 0.3980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 GLN C 376 HIS ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.181529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.114895 restraints weight = 50681.081| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.94 r_work: 0.3256 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28919 Z= 0.120 Angle : 0.745 46.463 39069 Z= 0.337 Chirality : 0.042 0.261 4658 Planarity : 0.004 0.050 4772 Dihedral : 12.576 172.412 5153 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.84 % Favored : 91.57 % Rotamer: Outliers : 3.24 % Allowed : 31.38 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 3548 helix: 1.63 (0.14), residues: 1612 sheet: 0.06 (0.45), residues: 149 loop : -2.11 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 443 TYR 0.012 0.001 TYR C 806 PHE 0.025 0.001 PHE D 253 TRP 0.009 0.001 TRP C 302 HIS 0.017 0.001 HIS C 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (28919) covalent geometry : angle 0.74532 / 0.34 (39069) hydrogen bonds : bond 0.03795 / 2.56 ( 1155) hydrogen bonds : angle 4.32792 / 3.05 ( 3390) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 192 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.1948 (OUTLIER) cc_final: 0.1726 (mt) REVERT: A 181 MET cc_start: 0.5957 (tpt) cc_final: 0.5623 (tpt) REVERT: A 380 HIS cc_start: 0.4898 (OUTLIER) cc_final: 0.4329 (p90) REVERT: A 479 GLU cc_start: 0.1693 (OUTLIER) cc_final: -0.2121 (tt0) REVERT: A 529 GLU cc_start: 0.5612 (OUTLIER) cc_final: 0.4883 (mm-30) REVERT: A 553 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8266 (ptpp) REVERT: A 571 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7936 (ttmm) REVERT: A 730 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8077 (tp) REVERT: A 748 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8100 (tm-30) REVERT: B 31 LYS cc_start: 0.5758 (OUTLIER) cc_final: 0.5151 (mmmt) REVERT: B 146 MET cc_start: 0.6538 (pmt) cc_final: 0.5776 (pp-130) REVERT: B 181 MET cc_start: 0.5829 (tpt) cc_final: 0.3052 (ptt) REVERT: B 258 LYS cc_start: 0.9396 (tptt) cc_final: 0.9038 (mtpt) REVERT: B 507 MET cc_start: 0.7244 (tpt) cc_final: 0.4882 (tmm) REVERT: B 535 MET cc_start: -0.0765 (OUTLIER) cc_final: -0.1287 (mpt) REVERT: B 748 GLU cc_start: 0.8894 (mm-30) cc_final: 0.7985 (tp30) REVERT: C 270 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: C 350 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7219 (tm-30) REVERT: C 376 HIS cc_start: 0.4661 (OUTLIER) cc_final: 0.4347 (p90) REVERT: C 471 MET cc_start: 0.3563 (tmt) cc_final: 0.2558 (mtt) REVERT: C 503 ASN cc_start: 0.8677 (t0) cc_final: 0.8281 (m-40) REVERT: C 505 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8390 (pp20) REVERT: C 532 MET cc_start: 0.5806 (pp-130) cc_final: 0.5592 (ttp) REVERT: D 37 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6656 (tm-30) REVERT: D 231 MET cc_start: 0.4547 (OUTLIER) cc_final: 0.2341 (mmt) REVERT: D 290 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8081 (t80) REVERT: D 423 LEU cc_start: 0.5322 (OUTLIER) cc_final: 0.5039 (mm) REVERT: D 445 MET cc_start: 0.7892 (mtp) cc_final: 0.7215 (ppp) REVERT: D 535 MET cc_start: 0.1412 (ptt) cc_final: -0.0004 (mtt) REVERT: D 538 LEU cc_start: 0.3632 (OUTLIER) cc_final: 0.2690 (tm) REVERT: D 570 ASP cc_start: 0.8540 (t0) cc_final: 0.7685 (p0) outliers start: 99 outliers final: 64 residues processed: 276 average time/residue: 0.6271 time to fit residues: 205.2360 Evaluate side-chains 269 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 187 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 749 GLU Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 656 ASP Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 895 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 101 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 288 optimal weight: 0.0770 chunk 187 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 138 optimal weight: 0.0980 chunk 338 optimal weight: 0.5980 chunk 201 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 HIS ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.181815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.115511 restraints weight = 50675.130| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.92 r_work: 0.3266 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28919 Z= 0.115 Angle : 0.746 46.448 39069 Z= 0.337 Chirality : 0.042 0.261 4658 Planarity : 0.004 0.051 4772 Dihedral : 12.361 172.606 5153 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.86 % Favored : 91.54 % Rotamer: Outliers : 2.91 % Allowed : 31.68 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3548 helix: 1.62 (0.14), residues: 1620 sheet: 0.11 (0.45), residues: 149 loop : -2.10 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 443 TYR 0.011 0.001 TYR C 806 PHE 0.018 0.001 PHE A 818 TRP 0.009 0.001 TRP D 817 HIS 0.016 0.001 HIS C 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (28919) covalent geometry : angle 0.74621 / 0.34 (39069) hydrogen bonds : bond 0.03679 / 2.48 ( 1155) hydrogen bonds : angle 4.29805 / 3.03 ( 3390) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 192 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.1988 (OUTLIER) cc_final: 0.1760 (mt) REVERT: A 181 MET cc_start: 0.5955 (tpt) cc_final: 0.5630 (tpt) REVERT: A 380 HIS cc_start: 0.4953 (OUTLIER) cc_final: 0.4377 (p90) REVERT: A 479 GLU cc_start: 0.1684 (OUTLIER) cc_final: -0.2116 (tt0) REVERT: A 529 GLU cc_start: 0.5585 (OUTLIER) cc_final: 0.4988 (mm-30) REVERT: A 553 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8266 (ptpp) REVERT: A 571 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7948 (ttmm) REVERT: A 730 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8073 (tp) REVERT: A 748 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8074 (tm-30) REVERT: B 31 LYS cc_start: 0.5738 (OUTLIER) cc_final: 0.5094 (mmmt) REVERT: B 146 MET cc_start: 0.6506 (pmt) cc_final: 0.5724 (pp-130) REVERT: B 181 MET cc_start: 0.5853 (tpt) cc_final: 0.3043 (ptt) REVERT: B 258 LYS cc_start: 0.9389 (tptt) cc_final: 0.9026 (mtpt) REVERT: B 316 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7988 (tp) REVERT: B 507 MET cc_start: 0.7150 (tpt) cc_final: 0.4842 (tmm) REVERT: B 535 MET cc_start: -0.0785 (OUTLIER) cc_final: -0.1287 (mpt) REVERT: B 748 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8006 (tp30) REVERT: C 270 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: C 350 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: C 376 HIS cc_start: 0.4656 (OUTLIER) cc_final: 0.4405 (p90) REVERT: C 471 MET cc_start: 0.3511 (tmt) cc_final: 0.2571 (mtt) REVERT: C 503 ASN cc_start: 0.8666 (t0) cc_final: 0.8281 (m-40) REVERT: C 505 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8371 (pp20) REVERT: C 532 MET cc_start: 0.5901 (pp-130) cc_final: 0.5696 (ttp) REVERT: D 37 GLU cc_start: 0.6870 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: D 146 MET cc_start: -0.0007 (tmt) cc_final: -0.0264 (mmt) REVERT: D 231 MET cc_start: 0.4454 (OUTLIER) cc_final: 0.2298 (mmt) REVERT: D 290 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8040 (t80) REVERT: D 423 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4889 (mm) REVERT: D 445 MET cc_start: 0.7910 (mtp) cc_final: 0.7237 (ppp) REVERT: D 535 MET cc_start: 0.1376 (ptt) cc_final: -0.0028 (mtt) REVERT: D 538 LEU cc_start: 0.3637 (OUTLIER) cc_final: 0.2684 (tm) REVERT: D 570 ASP cc_start: 0.8529 (t0) cc_final: 0.7763 (p0) REVERT: D 586 LYS cc_start: 0.8296 (tptt) cc_final: 0.8012 (tppt) outliers start: 89 outliers final: 58 residues processed: 267 average time/residue: 0.6099 time to fit residues: 193.7495 Evaluate side-chains 265 residues out of total 3056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 188 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 529 GLU Chi-restraints excluded: chain A residue 553 LYS Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 749 GLU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 749 GLU Chi-restraints excluded: chain B residue 766 MET Chi-restraints excluded: chain B residue 779 THR Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain C residue 61 TYR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 350 GLN Chi-restraints excluded: chain C residue 376 HIS Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 610 VAL Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 701 SER Chi-restraints excluded: chain C residue 741 ILE Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 828 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 654 SER Chi-restraints excluded: chain D residue 739 THR Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 895 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 162 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 306 optimal weight: 40.0000 chunk 276 optimal weight: 5.9990 chunk 203 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 HIS ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.180186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.112942 restraints weight = 50731.253| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.92 r_work: 0.3204 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28919 Z= 0.152 Angle : 0.762 46.507 39069 Z= 0.347 Chirality : 0.043 0.259 4658 Planarity : 0.004 0.051 4772 Dihedral : 12.449 172.033 5153 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.95 % Favored : 91.46 % Rotamer: Outliers : 2.95 % Allowed : 31.84 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 3548 helix: 1.61 (0.14), residues: 1608 sheet: 0.13 (0.45), residues: 150 loop : -2.11 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 375 TYR 0.014 0.001 TYR C 806 PHE 0.018 0.001 PHE A 818 TRP 0.008 0.001 TRP C 302 HIS 0.028 0.001 HIS C 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (28919) covalent geometry : angle 0.76222 / 0.35 (39069) hydrogen bonds : bond 0.04201 / 2.83 ( 1155) hydrogen bonds : angle 4.37648 / 3.08 ( 3390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18426.99 seconds wall clock time: 312 minutes 15.26 seconds (18735.26 seconds total)